Building a Crop Yield Prediction App Using Satellite Imagery and Jupyter

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May 31, 2022
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Building a Crop Yield Prediction App Using Satellite Imagery and Jupyter

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A team of 30 AI engineers used Google Earth Engine (GEE) images and Jupyter to build an app for crop yield prediction in Senegal, Africa, to improve food security in the country.

Execution time: 0.0012 seconds

ACF

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value<p><a href="#omdena-crop-yield-prediction-ai-challenge-in-africa">Omdena´s Crop Yield Prediction AI Challenge in Africa</a></p> <p><a href="#challenges-encountered">Challenges Encountered</a></p> <p><a href="#creating-the-application">Creating the Application</a></p> <ul> <li><a href="#step-1-define-the-user-interface">Step 1: Define the user interface</a></li> <li><a href="#step-2-updating-the-widgets">Step 2: Updating the widgets</a></li> <li><a href="#step-3-create-the-app-layout">Step 3: Create the app layout</a></li> </ul> <p><a href="#steps-to-run-the-application">Steps to run the application</a></p> <p><a href="#check-out-the-2-mins-app-demo">Check out the 2 mins app demo</a></p> <p><a href="#useful-resources">Useful resources</a></p>
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Execution time: 0.0012 seconds

Omdena´s Crop Yield Prediction AI Challenge in Africa

In this Omdena AI Challenge with the Global Partnership for Sustainable Development Data, we created a simple but powerful application using GEE images to estimate crop yield in Senegal.

For food security understanding the food system is essential. Accurate crop type details in near real-time will provide policymakers insights on the food system and will provide information on crop diversity and nutrition outcomes. So we created an application using open-source satellite images to identify the crops and estimate the yields for any given area.

Build your portfolio with real-world projects from Omdena

Challenges Encountered

1. The first challenge is to acquire satellite images from the regions selected by the user interactively over a map.

For this, we came up with the Python package Geemap which allows users to select a region in the map and get the geo-coordinates of the selected region.

!pip install geemap
import geemap
Map = geemap.Map()
Selecting a region from the map .  Source: Omdena

Selecting a region from the map.  Source: Omdena


#draw a rectangle in the above map and then run this
#ROI - Region of Interest
feature = Map.draw_last_feature
ROI = feature.geometry()
ROI.getInfo()

Output:

{'geodesic': False,
 'type': 'Polygon',
 'coordinates': [[[-120.021748, 46.126847],
   [-120.021748, 46.126957],
   [-120.021535, 46.126957],
   [-120.021535, 46.126847],
   [-120.021748, 46.126847]]]}

2. Downloading the geo tiff file and processing the file to get the data in the form of a matrix is computationally powerful.

We used the Geemap function ‘ee_to_numpy’ for this. It converts the image collected from the Google earth engine ‘ee.image’ into ‘NumPy’ array. It doesn’t need local computational power. It is all done in Google Earth Engine itself.

import ee
def maskS2clouds(image):
  qa = image.select('QA60')
  cloudBitMask = 1 << 10
  cirrusBitMask = 1 << 11
  mask = qa.bitwiseAnd(cloudBitMask).eq(0).And(
             qa.bitwiseAnd(cirrusBitMask).eq(0))
  return image.updateMask(mask).divide(10000) 


# Load Sentinel-2 TOA reflectance data.
imageCollection = ee.ImageCollection('COPERNICUS/S2') \
    .filterDate('2016-01-01', '2016-12-31') \
    .filter(ee.Filter.lt('CLOUDY_PIXEL_PERCENTAGE', 5)) \
    .map(maskS2clouds) \
    .filterBounds(roi) \
    .sort('CLOUDY_PIXEL_PERCENTAGE')


rawImg = ee.Image(imageCollection.toList(imageCollection.size()).get(0))

#get the matrix for B2 band only
B2_image = geemap.ee_to_numpy(rawImg.select(['B2']), region=ROI)

3. Each band in the sentinel is of a different resolution. So the matrix we got is of different shapes for each resolution. We wanted to have all the matrices stacked on top of each other to get a single multi-channel image.

Sentinel Dataset Band Info .  Source: Google Earth Engine Data Catalog

Sentinel Dataset Band Info.  Source: Google Earth Engine Data Catalog

We resized all the matrix to the high resolution (In this case 10 meters resolution) using the ‘nearest neighbor interpolation’ method.

targetSize = (50,50)
B5_Matrix = cv2.resize(B5_image,targetSize,interpolation=cv2.INTER_NEAREST)
Source: Omdena

Source: Omdena

Creating the Application

To create the application we used ‘ipywidgets’ which is an interactive HTML widget for Jupyter Notebook, Jupyter Lab, and Ipython Kernel. Then we used Voilà to turn the Jupyter notebooks into standalone web applications.

Step 1:  Define the user interface

Sample code

#Date picker 
dateBox = widgets.DatePicker(
    description='',
    disabled=False
)

#Map
mapWidget = widgets.Output()
    
#labels
step1 = widgets.Label('Step 1: Select the date')
step2 = widgets.Label('Step 2: Select Region from the map')
step3 = widgets.Label('Step 3: Load model')
step4 = widgets.Label('Step 4: Estimate yield')
estimate_yield_debug = widgets.Label('')
#Buttons
getROI = widgets.Button(description='Ok')
estimate_yield_Btn = widgets.Button(description='Estimate yield')
loadModel_Btn = widgets.Button(description='Load model')

#Progress bar
progressBar = widgets.IntProgress(
    value=0,
    min=0,
    max=19,
    step=1,
    description='',
    bar_style='info', 
    orientation='horizontal'
)

#Text Area
estimate_yield_Out = widgets.Textarea(
    value='',
    placeholder='',
    description='',
    disabled=True,
    layout={'height': '300px'}
)

#Display prediction image (Matplotlib plot)
estimate_yield_plot = widgets.Output()

Step 2:  Updating the widgets

1. Updating a label

for band in bands:
    estimate_yield_debug.value = f"Processing: {band}"
Source: Omdena

Source: Omdena

2. Reading information from date Picker

year  = dateBox.value.year
month = dateBox.value.month
day   = dateBox.value.day
Source: Omdena

Source: Omdena

3. To display Map

Map = geemap.Map(center=[14.607989,-14.531731], zoom=7)
Map.add_basemap('Google Satellite Hybrid')
with mapWidget:
    display(Map)

4. To trigger a function when a button is clicked

def getStatistics(change):
      """
      some codes
      """    
getROI.on_click(getStatistics)

5. To update the progress bar

for band in bands:
      estimate_yield_debug.value = f"Processing: {band}"
      #Update progress bar
      progressBar.value = progressBar.value +1
Source: Omdena

Source: Omdena

6. To display matplot image

def plotResult(prediction):
    """
    Code to visualize the prediction in the form of Matplotlib image.
    """

    
    #display output
    plt.show()
#Visualize the prediction
with estimate_yield_plot:
      plotResult(prediction)
Using Jupyter Notebook to make a crop yield app. Source: Omdena

Using Jupyter Notebook to make a crop yield app. Source: Omdena

Step 3:  Create the app layout

Vertical Box (widgets.VBox) and Horizontal Box (widgets.HBox) are used to group widgets together.

Then we can use AppLayout from ipywidgets to align all the widgets in a proper way.

from ipywidgets import AppLayout
#Arrange the layout
verticalBox = mapWidget
vBox1 = widgets.VBox([step1, dateBox,vBox])
vBox2 = widgets.VBox([step2, getROI,
                      step3,loadModel_Btn,                            step4,estimate_yield_Btn,progressBar,estimate_yield_debug,yieldOutput,
                      estimate_yield_Out,estimate_yield_plot])

AppLayout(header=None,
          left_sidebar=vBox1,
          right_sidebar=vBox2,
          footer=None,
          height="70%", width="150%")

Steps to run the application

1. Open the notebook

Using Jupyter Notebook to make a crop yield app. Source: Omdena

Using Jupyter Notebook to make a crop yield app. Source: Omdena

2. Click on the Voilà button

Voila button in Jupyter Notebook to make a crop yield app - Source: Omdena

Voila button in Jupyter Notebook to make a crop yield app – Source: Omdena

Check out the 2 mins app demo

Useful resources

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border_radiion|100%|100%|100%|100%
border_radii_tableton||||
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Praveen Kanna

Execution time: 0.0062 seconds

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global_colors_info{}

Praveen Kanna

Execution time: 0.0010 seconds

Execution time: 0.0003 seconds

ACF

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Module Settings

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text_before_css_line_height1em
seperator_text_alignleft
seperator_font_size14px
seperator_letter_spacing0px
seperator_line_height1em
relational_field_item_text_alignleft
relational_field_item_font_size14px
relational_field_item_letter_spacing0px
relational_field_item_line_height1em
background_enable_coloron
use_background_color_gradientoff
background_color_gradient_repeatoff
background_color_gradient_typelinear
background_color_gradient_direction180deg
background_color_gradient_direction_radialcenter
background_color_gradient_stops#2b87da 0%|#29c4a9 100%
background_color_gradient_unit%
background_color_gradient_overlays_imageoff
background_color_gradient_start#2b87da
background_color_gradient_start_position0%
background_color_gradient_end#29c4a9
background_color_gradient_end_position100%
background_enable_imageon
parallaxoff
parallax_methodon
background_sizecover
background_image_widthauto
background_image_heightauto
background_positioncenter
background_horizontal_offset0
background_vertical_offset0
background_repeatno-repeat
background_blendnormal
background_enable_video_mp4on
background_enable_video_webmon
allow_player_pauseoff
background_video_pause_outside_viewporton
background_enable_pattern_styleoff
background_pattern_stylepolka-dots
background_pattern_colorrgba(0,0,0,0.2)
background_pattern_sizeinitial
background_pattern_widthauto
background_pattern_heightauto
background_pattern_repeat_origintop_left
background_pattern_horizontal_offset0
background_pattern_vertical_offset0
background_pattern_repeatrepeat
background_pattern_blend_modenormal
background_enable_mask_styleoff
background_mask_stylelayer-blob
background_mask_color#ffffff
background_mask_aspect_ratiolandscape
background_mask_sizestretch
background_mask_widthauto
background_mask_heightauto
background_mask_positioncenter
background_mask_horizontal_offset0
background_mask_vertical_offset0
background_mask_blend_modenormal
custom_buttonon
button_text_size14px
button_bg_use_color_gradientoff
button_bg_color_gradient_repeatoff
button_bg_color_gradient_typelinear
button_bg_color_gradient_direction180deg
button_bg_color_gradient_direction_radialcenter
button_bg_color_gradient_stops#2b87da 0%|#29c4a9 100%
button_bg_color_gradient_unit%
button_bg_color_gradient_overlays_imageoff
button_bg_color_gradient_start#2b87da
button_bg_color_gradient_start_position0%
button_bg_color_gradient_end#29c4a9
button_bg_color_gradient_end_position100%
button_bg_enable_imageon
button_bg_parallaxoff
button_bg_parallax_methodon
button_bg_sizecover
button_bg_image_widthauto
button_bg_image_heightauto
button_bg_positioncenter
button_bg_horizontal_offset0
button_bg_vertical_offset0
button_bg_repeatno-repeat
button_bg_blendnormal
button_bg_enable_video_mp4on
button_bg_enable_video_webmon
button_bg_allow_player_pauseoff
button_bg_video_pause_outside_viewporton
button_border_width0px
button_use_iconoff
button_icon_placementright
button_on_hoveron
button_custom_padding0px|0px|0px|0px|true|true
positioningnone
position_origin_atop_left
position_origin_ftop_left
position_origin_rtop_left
text_orientationleft
widthauto
max_widthnone
module_alignmentleft
min_heightauto
heightauto
max_heightnone
custom_margin_tablet||10px||false|false
custom_margin_phone||10px||false|false
custom_margin_last_editedon|tablet
filter_hue_rotate0deg
filter_saturate100%
filter_brightness100%
filter_contrast100%
filter_invert0%
filter_sepia0%
filter_opacity100%
filter_blur0px
mix_blend_modenormal
animation_stylenone
animation_directioncenter
animation_duration1000ms
animation_delay0ms
animation_intensity_slide50%
animation_intensity_zoom50%
animation_intensity_flip50%
animation_intensity_fold50%
animation_intensity_roll50%
animation_starting_opacity0%
animation_speed_curveease-in-out
animation_repeatonce
hover_transition_duration300ms
hover_transition_delay0ms
hover_transition_speed_curveease
link_option_url_new_windowoff
sticky_positionnone
sticky_offset_top0px
sticky_offset_bottom0px
sticky_limit_topnone
sticky_limit_bottomnone
sticky_offset_surroundingon
sticky_transitionon
motion_trigger_startmiddle
hover_enabled0
title_css_text_align_tabletcenter
title_css_text_align_phonecenter
title_css_text_align_last_editedon|phone
acf_label_css_text_align_tabletcenter
acf_label_css_text_align_phonecenter
acf_label_css_text_align_last_editedon|tablet
label_css_text_align_tabletcenter
label_css_text_align_phonecenter
label_css_text_align_last_editedon|desktop
relational_field_item_text_align_tabletcenter
relational_field_item_text_align_phonecenter
relational_field_item_text_align_last_editedon|tablet
text_orientation_tabletcenter
text_orientation_phonecenter
text_orientation_last_editedon|phone
module_alignment_tabletcenter
module_alignment_phonecenter
module_alignment_last_editedon|desktop
custom_css_main_elementdisplay:block;
title_css_text_shadow_stylenone
title_css_text_shadow_horizontal_length0em
title_css_text_shadow_vertical_length0em
title_css_text_shadow_blur_strength0em
title_css_text_shadow_colorrgba(0,0,0,0.4)
acf_label_css_text_shadow_stylenone
acf_label_css_text_shadow_horizontal_length0em
acf_label_css_text_shadow_vertical_length0em
acf_label_css_text_shadow_blur_strength0em
acf_label_css_text_shadow_colorrgba(0,0,0,0.4)
label_css_text_shadow_stylenone
label_css_text_shadow_horizontal_length0em
label_css_text_shadow_vertical_length0em
label_css_text_shadow_blur_strength0em
label_css_text_shadow_colorrgba(0,0,0,0.4)
text_before_css_text_shadow_stylenone
text_before_css_text_shadow_horizontal_length0em
text_before_css_text_shadow_vertical_length0em
text_before_css_text_shadow_blur_strength0em
text_before_css_text_shadow_colorrgba(0,0,0,0.4)
seperator_text_shadow_stylenone
seperator_text_shadow_horizontal_length0em
seperator_text_shadow_vertical_length0em
seperator_text_shadow_blur_strength0em
seperator_text_shadow_colorrgba(0,0,0,0.4)
relational_field_item_text_shadow_stylenone
relational_field_item_text_shadow_horizontal_length0em
relational_field_item_text_shadow_vertical_length0em
relational_field_item_text_shadow_blur_strength0em
relational_field_item_text_shadow_colorrgba(0,0,0,0.4)
button_text_shadow_stylenone
button_text_shadow_horizontal_length0em
button_text_shadow_vertical_length0em
button_text_shadow_blur_strength0em
button_text_shadow_colorrgba(0,0,0,0.4)
box_shadow_stylenone
box_shadow_colorrgba(0,0,0,0.3)
box_shadow_positionouter
box_shadow_style_buttonnone
box_shadow_color_buttonrgba(0,0,0,0.3)
box_shadow_position_buttonouter
text_shadow_stylenone
text_shadow_horizontal_length0em
text_shadow_vertical_length0em
text_shadow_blur_strength0em
text_shadow_colorrgba(0,0,0,0.4)
disabledoff
global_colors_info{}
custom_css_main_element_last_editedon|phone
custom_css_main_element_tabletdisplay:block;
custom_css_main_element_phonedisplay:block;

Execution time: 0.0013 seconds

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5 Comments
  1. joseph

    Hi
    Nice article!
    is there a github repo with the code and data you used?

    Reply
  2. Issam Boukhris

    Thank you for this nice article.

    Is there any github repository where I can find the script you used ?

    With Thanks

    Reply
    • Valentin

      Nice work! Congratulations.
      I am interested with the python script used to predict the yields, please.

      Thank you

      Reply
  3. Rocco

    Can you provide the complete python code for this great app?

    Thank you

    Reply
  4. Dishan Otieno

    Great work

    Reply
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